The invention discloses a method for preparing high-purity chlorogenic acid from potato skins, and belongs to the technical field of agricultural product waste utilization. The method for preparing the high-purity chlorogenic acid mainly comprises the following steps: (1) the fresh potato skins are dried and crushed, and then extracted through an ethanol solution; (2) an extracting solution is decompressed and concentrated to be dry and then separated and purified through macroporous resin; and (3) the high-purity chlorogenic acid can be prepared through high-speed counter-current chromatography purification. Waste is turned into wealth, the high-speed counter-current chromatography preparation method is innovatively adopted to prepare the high-purity chlorogenic acid from the potato skins, the preparation time is short, and the efficiency and purity are high; and in addition, ethanol, ethyl acetate and acetic acid solvents adopted in extraction, separation and preparation of chlorogenic acid substances are low in toxicity and good in volatility, and the obtained high-purity chlorogenic acid contains no residue, and can be used as ingredients of the industries such as food, cosmetics, health tea and edible oil.